Chapter 11: Data Formats of the Proteomics Standards Initiative

The existence and adoption of data standards in computational proteomics, as in any other field, is generally perceived to be crucial for the further development of the discipline. We here give an up-to-date overview of the open standard data formats that have been developed under the umbrella of the Proteomics Standards Initiative (PSI). We will focus in those formats related to mass spectrometry (MS). Most of them are based in XML (Extensible Markup Language) schemas: mzML (for primary MS data, the output of mass spectrometers), mzIdentML (for peptide and protein identification data), mzQuantML (for peptide and protein quantification data) and TraML (for reporting transition lists for selected reaction monitoring approaches). In addition, mzTab was developed as a simpler tab-delimited file to support peptide, protein and small molecule identification and quantification data in the same file. In all cases, we will explain the main characteristics of each format, describe the main existing software implementations and give an update of the ongoing work to extend the formats to support new use cases. Additionally, we will discuss other data formats that have been inspired by the PSI formats. Finally, other PSI data standard formats (not MS related) will be also outlined in brief.